This study aimed to comprehensively investigate the reliability of multiple heart rate variability (HRV) parameters, and to explore the influence of artefact removal and breathing condition on HRV reliability. Resting HRV was collected using Polar Team2 monitors on forty-one participants (age: 19.9±1.2 years; 28 females, 13 males) during two separate days. Within each session, participants performed 10 minutes each of spontaneous and controlled breathing (randomized order). Kubios HRV analysis software was used to analyze 180s data epochs using “low” or “strong” artefact removal. Relative reliability was assessed using intraclass correlation coefficients (ICC2,1) and absolute reliability was quantified using mean-normalized standard error of measurement (SEM%). Time domain and nonlinear parameters produced poor to good inter-session agreement (ICC:0.34–0.68; SEM%: 11.0–39.0) with “low” artefact removal, regardless of breathing condition. Frequency domain parameters demonstrated fair inter-session agreement during controlled breathing (ICC:0.40–0.45; SEM%: 26.0–70.0), but poor agreement during spontaneous breathing (ICC:0.07–0.13; SEM%: 32.0–81.0). Minimal differences in ICCs were observed between “low” and “strong” artefact removal. Thus, this study provides three practical applications: 1) HRV monitoring is most reliable when using time domain and nonlinear parameters, regardless of breathing or filtering condition, but no single parameter is especially reliable. The large variation and poor inter-session reliability of frequency indices during spontaneous breathing are improved by controlling breathing rate; 2) “Low” artefact removal appears superior to more aggressive artefact removal; and 3) Inter-session differences in HRV measurements <30% may be indicative of normal daily variation rather than true physiologic changes.